Regenerate artifacts from biolink-model.yaml

project/graphql/biolink_model.graphql

@@ -3527,6 +3527,7 @@ type GeneToExpressionSiteAssociation
     category: [Uriorcurie]
     stageQualifier: LifeStage
     quantifierQualifier: OntologyClass
+    objectSpecializationQualifier: Uriorcurie
     subject: GeneOrGeneProduct!
     object: AnatomicalEntity!
     predicate: PredicateType!

project/jsonld/biolink_model.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2025-01-17T17:31:36",
+      "generation_date": "2025-01-31T19:01:54",
       "source": "biolink_model.yaml"
    },
    "@context": {

project/jsonld/biolink_model.jsonld

@@ -4383,9 +4383,10 @@
       "is_a": "specialization_qualifier",
       "domain": "Association",
       "slot_uri": "https://w3id.org/biolink/vocab/object_specialization_qualifier",
-      "owner": "EntityToDiseaseOrPhenotypicFeatureAssociationMixin",
+      "owner": "GeneToExpressionSiteAssociation",
       "domain_of": [
-        "EntityToDiseaseOrPhenotypicFeatureAssociationMixin"
+        "EntityToDiseaseOrPhenotypicFeatureAssociationMixin",
+        "GeneToExpressionSiteAssociation"
       ],
       "range": "uriorcurie",
       "@type": "SlotDefinition"
@@ -34529,6 +34530,7 @@
         "association_category",
         "gene_to_expression_site_association_stage_qualifier",
         "gene_to_expression_site_association_quantifier_qualifier",
+        "object_specialization_qualifier",
         "gene_to_expression_site_association_subject",
         "gene_to_expression_site_association_object",
         "gene_to_expression_site_association_predicate"
@@ -35901,9 +35903,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "biolink_model.yaml",
-  "source_file_date": "2025-01-17T17:31:33",
-  "source_file_size": 404136,
-  "generation_date": "2025-01-17T17:31:39",
+  "source_file_date": "2025-01-31T19:01:51",
+  "source_file_size": 404176,
+  "generation_date": "2025-01-31T19:01:57",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/biolink_model.context.jsonld",

project/jsonschema/biolink_model.schema.json

@@ -23109,6 +23109,13 @@
                         "null"
                     ]
                 },
+                "object_specialization_qualifier": {
+                    "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the  subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept  and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.",
+                    "type": [
+                        "string",
+                        "null"
+                    ]
+                },
                 "original_object": {
                     "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.",
                     "type": [

project/protobuf/biolink_model.proto

@@ -3185,6 +3185,7 @@ message GeneToExpressionSiteAssociation
  repeated  uriorcurie category = 0
   lifeStage stageQualifier = 0
   ontologyClass quantifierQualifier = 0
+  uriorcurie objectSpecializationQualifier = 0
   geneOrGeneProduct subject = 0
   anatomicalEntity object = 0
   predicateType predicate = 0

project/shex/biolink_model.shex

@@ -2392,6 +2392,7 @@ linkml:Sparqlpath xsd:string
           rdf:type [ <Association> ] ? ;
           <stage_qualifier> @<LifeStage> ? ;
           <quantifier_qualifier> @<OntologyClass> ? ;
+          <object_specialization_qualifier> @linkml:Uriorcurie ? ;
           rdf:subject @<GeneOrGeneProduct> ;
           rdf:object @<AnatomicalEntity> ;
           rdf:predicate @<PredicateType>

src/biolink_model/datamodel/model.py

@@ -1,5 +1,5 @@
 # Auto generated from biolink_model.yaml by pythongen.py version: 0.0.1
-# Generation date: 2025-01-17T17:31:52
+# Generation date: 2025-01-31T19:02:09
 # Schema: Biolink-Model
 #
 # id: https://w3id.org/biolink/biolink-model
@@ -12117,6 +12117,7 @@ class GeneToExpressionSiteAssociation(Association):
     predicate: Union[str, PredicateType] = None
     stage_qualifier: Optional[Union[str, LifeStageId]] = None
     quantifier_qualifier: Optional[Union[str, OntologyClassId]] = None
+    object_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.id):
@@ -12145,6 +12146,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.quantifier_qualifier is not None and not isinstance(self.quantifier_qualifier, OntologyClassId):
             self.quantifier_qualifier = OntologyClassId(self.quantifier_qualifier)
 
+        if self.object_specialization_qualifier is not None and not isinstance(self.object_specialization_qualifier, URIorCURIE):
+            self.object_specialization_qualifier = URIorCURIE(self.object_specialization_qualifier)
+
         super().__post_init__(**kwargs)
         if not isinstance(self.category, list):
             self.category = [self.category] if self.category is not None else []

src/biolink_model/datamodel/pydanticmodel_v2.py

@@ -7372,6 +7372,7 @@ class GeneToExpressionSiteAssociation(Association):
     """
     stage_qualifier: Optional[str] = Field(None, description="""stage at which the gene is expressed in the site""")
     quantifier_qualifier: Optional[str] = Field(None, description="""can be used to indicate magnitude, or also ranking""")
+    object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the  subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept  and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""")
     subject: str = Field(..., description="""Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location.""")
     predicate: str = Field(..., description="""expression relationship""")
     object: str = Field(..., description="""location in which the gene is expressed""")

src/biolink_model/schema/biolink_model.yaml

@@ -11163,6 +11163,7 @@ classes:
     slots:
       - stage qualifier
       - quantifier qualifier
+      - object specialization qualifier
     slot_usage:
       subject:
         range: gene or gene product

src/biolink_model/scripts/classprefixes.py

@@ -1,5 +1,5 @@
 # Auto generated from class_prefixes.yaml by pythongen.py version: 0.0.1
-# Generation date: 2025-01-17T17:32:37
+# Generation date: 2025-01-31T19:02:53
 # Schema: BiolinkClassPrefixes
 #
 # id: biolink-model-class-prefixes